cBioPortal validation report

Study directory:
./generated_data/tcga/read_tcga_gdc

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 5.4.7-dirty-SNAPSHOT

Validation status: Failed
Line Number Column Number Message Value Encountered
Debug – – Requesting info from portal at 'https://www.cbioportal.org' –
Debug – – Requesting cancer-types from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genes from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genesets from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genesets_version from portal at 'https://www.cbioportal.org' –
Debug – – Requesting gene-panels from portal at 'https://www.cbioportal.org' –
Debug – – Retrieving chromosome lengths from '/home/koj2/playground/nci-crdc-pipeline/scripts/importer/chromosome_sizes.json' –
Error – – Cancer type of study is neither known to the portal nor defined in a cancer_type file READ
Debug – – Validating case lists –
Info – – Validation of case list folder complete –
Info – – Validation complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Error – – Multiple case lists with this stable_id defined in the study read_tcga_gdc_all (already defined in meta_study.txt)
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 14, 78 1 Clinical data defined for a patient with no samples TCGA-AF-3912, TCGA-AG-4009
Info – – Validation of file complete –
Info – – Read 177 lines. Lines with warning: 2. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Info – – Validation of file complete –
Info – – Read 176 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 86, 178, 179… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1733 values
Info – – Validation of file complete –
Info – – Read 38456 lines. Lines with warning: 1733. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 13717, 39683, 47019… – Segment is zero bases wide and will not be loaded 10131410-10131410, 5959081-5959081, 92526718-92526718… See all 4 values
Info – – Validation of file complete –
Info – – Read 52132 lines. Lines with warning: 4. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1848 values
Info – – Validation of file complete –
Info – – Read 40760 lines. Lines with warning: 1848. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1848 values
Info – – Validation of file complete –
Info – – Read 40760 lines. Lines with warning: 1848. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1848 values
Info – – Validation of file complete –
Info – – Read 40760 lines. Lines with warning: 1848. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1848 values
Info – – Validation of file complete –
Info – – Read 40760 lines. Lines with warning: 1848. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 3 – Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view –
Info 5, 16, 19… – Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] Silent, 3'Flank, RNA… See all 13748 values
Warning 694, 902, 1937… – Entrez gene id exists, but gene symbol specified is not known to the cBioPortal instance. The gene symbol will be ignored. Might be wrong mapping, new or deprecated gene symbol. RNF165, FAM214A, C11ORF45… See all 97 values
Warning 974, 2825, 9310… – Gene symbol not known to the cBioPortal instance. This record will not be loaded. C8ORF31, FAM160B1, LRRC6… See all 8 values
Warning 35856, 43477, 54182 – No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag –
Warning 52151 – Gene specification (Gene symbol 'Unknown', Entrez gene ID 0) for this variant implies intergenic even though Variant_Classification is not 'IGR' or 'Targeted_Region'; this variant will be filtered out RNA
Info – – Validation of file complete –
Info – – Read 57702 lines. Lines with warning: 110. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Error – – Invalid stable id for genetic_alteration_type 'MRNA_EXPRESSION', data_type 'CONTINUOUS'; expected one of [mrna_U133, rna_seq_mrna, rna_seq_v2_mrna, rna_seq_v2_mrna_median_normals, mirna, mrna, rna_seq_mrna_capture, mrna_seq_cpm, mrna_seq_tpm, mrna_seq_fpkm_capture, mrna_seq_fpkm_polya] mrna_seq_fpkm
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Error – – Invalid stable id for genetic_alteration_type 'MRNA_EXPRESSION', data_type 'Z-SCORE'; expected one of [mrna_U133_Zscores, rna_seq_mrna_median_Zscores, mrna_median_Zscores, rna_seq_v2_mrna_median_Zscores, rna_seq_v2_mrna_median_normals_Zscores, mirna_median_Zscores, mrna_merged_median_Zscores, mrna_zbynorm, mrna_seq_tpm_Zscores, mrna_seq_cpm_Zscores, rna_seq_mrna_capture_Zscores, mrna_seq_fpkm_capture_Zscores, mrna_seq_fpkm_polya_Zscores, mrna_U133_all_sample_Zscores, mrna_all_sample_Zscores, rna_seq_mrna_median_all_sample_Zscores, mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores, mrna_seq_cpm_all_sample_Zscores, mrna_seq_tpm_all_sample_Zscores, rna_seq_mrna_capture_all_sample_Zscores, mrna_seq_fpkm_capture_all_sample_Zscores, mrna_seq_fpkm_polya_all_sample_Zscores, mrna_seq_fpkm_Zscores, mrna_seq_fpkm_all_sample_Zscores] mrna_seq_read_counts_Zscores
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Warning – – Unrecognized field in meta file short_name
Info – – Validation of meta file complete –
Info – – Setting reference genome to human (GRCh38, hg38) –

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script